Codon usage patterns distort phylogenies from or of DNA sequences

Papers reporting phylogenetic reconstructions often include discussion of the nature of third position substitutions and have often treated third position data differently from other data. This paper extends such considerations. Plant biotechnologists interested in high levels of expression of foreign proteins have accumulated information on preferences for otherwise synonymous codons. This paper presents a simple analysis for codon bias. Not only is bias frequent, but bias also varies between cohorts of proteins, both by amino acid and by taxon. Analysis of codon usage in the parallel divergence of phytochromes in three model plants finds identical bias for all family members within each taxon and increasingly divergent patterns of bias between increasingly divergent taxa. The molecular constraint of taxon‐specific pools of tRNA molecules means individual triplets in a coding sequence are often not independent; algorithms designed to analyze independent characters are inappropriate for such data. Although a misestimate of the number of differences between taxa and groups of taxa can still generate an accurate description of the nesting of clades, other phylogenetic parameters will be strongly affected. Importantly, since codon bias produces smaller‐than‐expected within‐taxon variance (common use of favored triplets) and larger‐than‐expected between‐taxa variance (different favorites in different taxa), statistical support for nodes is certain to be wrong. The translational control of gene expression mediated by codon bias has implications for modern molecular systematics.